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Daniel Pedro de Jesus Faria é Professor Auxiliar no Departamento de Engenharia Informática do Instituto Superior Técnico, Universidade de Lisboa. É Doutorado em Informática, Especialidade Bioinformática pela Faculdade de Ciências da Universidade de Lisboa (2012) e Licenciado em Engenharia Biológica pelo Instituto Superior Técnico (2004). Publicou 25 artigos em revistas ou conferências internacionais com revisão por pares, e participou em 7 projetos de investigação com financiamento Europeu ou nacional. Desenvolve investigação nas áreas da web semântica, engenharia de conhecimento, integração de informação e bioinformática. É co-fundador e coordenador científico do programa de treino Ready for BioData Managament, dedicado à capacitação em gestão de dados da comunidade científica nacional. É também autor principal da ferramenta de mapeamento de ontologias AgreementMakerLight, que teve regularmente o melhor desempenho na competição internacional Ontology Alignment Evaluation Initiative entre 2014 e 2022 e foi por duas vezes premiada.
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Identification

Personal identification

Full name
Daniel Pedro de Jesus Faria

Citation names

  • Faria, Daniel

Author identifiers

Ciência ID
F712-80BD-030D
ORCID iD
0000-0003-1511-277X

Email addresses

  • daniel.faria@tecnico.ulisboa.pt (Professional)

Knowledge fields

  • Exact Sciences - Computer and Information Sciences
  • Exact Sciences - Computer and Information Sciences - Bioinformatics

Languages

Language Speaking Reading Writing Listening Peer-review
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
Spanish; Castilian Beginner (A1) Beginner (A1) Beginner (A1) Beginner (A1)
French Beginner (A1) Beginner (A1) Beginner (A1) Beginner (A1)
Education
Degree Classification
2007/01/01 - 2012/09/28
Concluded
 Doutoramento em Informática, Especialidade Bioinformática (Doutoramento)
Universidade de Lisboa Faculdade de Ciências, Portugal
"Automated Knowledge Extraction From Protein Sequence" (THESIS/DISSERTATION)
 N/A
2006/06/30
Concluded
 Curso pós-graduado de especialização em Bioinformática (Pós-Graduação)
Universidade de Lisboa Faculdade de Ciências, Portugal
"N/A" (THESIS/DISSERTATION)
 18
2004/10/31
Concluded
 Licenciatura em Engenharia Biológica (Licenciatura)
Universidade de Lisboa Instituto Superior Técnico, Portugal
"N/A" (THESIS/DISSERTATION)
 15
Affiliation

Science

Category
Host institution 		Employer
2022/10/06 - Current Researcher (Research) Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2021/02/19 - 2022/10/05 Contracted Researcher (Research) Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
2019/09/01 - 2021/01/31 Postdoc (Research) Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2015/06/01 - 2019/08/31 Postdoc (Research) Instituto Gulbenkian de Ciência, Portugal
Instituto Gulbenkian de Ciência, Portugal
2012/10/01 - 2014/10/31 Postdoc (Research) Universidade de Lisboa Faculdade de Ciências, Portugal
Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal

Teaching in Higher Education

Category
Host institution 		Employer
2022/10/06 - Current Assistant Professor (University Teacher) Universidade de Lisboa Instituto Superior Técnico, Portugal
2022/02/01 - 2022/06/30 Invited Assistant Professor (University Teacher) Universidade Católica Portuguesa, Portugal
2021/02/01 - 2021/07/31 Invited Assistant Professor (University Teacher) Universidade de Lisboa Instituto Superior Técnico, Portugal
Projects

Grant

Designation Funders
2019/09/01 - Current ELIXIR - Data for Life  European Life Sciences Infrastructure for Biological Information
info:eu-repo/grantAgreement/AKA/271642/FI
Post-doc Fellow
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
 Universidade do Algarve Faculdade de Ciências e Tecnologia
Ongoing
2022/06/01 - 2027/05/31 AgroServ: Integrated SERvices supporting a sustainable AGROecological transition
101058020
Researcher
European Union
2020/06/01 - 2020/12/31 VITACOV: Vitamin D-related polymorphisms and vitamin D levels as risk biomarkers of COVID-19 infection severity
613401452
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Concluded
2015/09/01 - 2019/08/31 ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences.
info:eu-repo/grantAgreement/EC/H2020/676559/EU
Post-doc Fellow
Instituto Gulbenkian de Ciência, Portugal
 Universidade do Algarve Faculdade de Ciências e Tecnologia
Concluded
2012/10/01 - 2014/10/29 SOMER: Semantic Ontology Matching using External Resources
info:eu-repo/grantAgreement/FCT/3599-PPCDT/119119/PT
Post-doc
Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal
 Universidade do Algarve Faculdade de Ciências e Tecnologia
Concluded

Contract

Designation Funders
2024/01/01 - Current DATAREX - Data Management for Research in ELIXIR
2023-COMM-DATAREX
BioData.pt, Portugal
Ongoing
2024/01 - Current Building bridges to foster the ambition to reach the frontiers of science with global significance and impact: collaboration between the Office of Data Science Strategy (ODSS) at the US National Institutes of Health (NIH) and ELIXIR
ELIXIR Staff Exchange NIH/ODSS
BioData.pt, Portugal
Ongoing
2023/09/01 - 2026/08/31 O aquecimento global ameaça a sustentabilidade da cultura do café através da infertilidade floral. Uma visão integrada para desvendar as pertubações no desenvolvimento floral e o potencial efeito protector do CO2 atmosférico elevado
10.54499/2022.01547.PTDC
2022.01547.PTDC
Universidade de Lisboa Instituto Superior de Agronomia, Portugal

Universidade Federal de Viçosa, Brazil

FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal

Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Universidade Federal de Lavras, Brazil

Universidade Nova de Lisboa Associação para a Inovação e Desenvolvimento da FCT, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2021/03/01 - 2024/02/29 Data sciEnce Tools for Epidemiologic surveillance using multiple sourCes of daTa - Improved flu/COVID-19 tracking and detection of new outbreaks
DSAIPA/DS/0133/2020
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2007/01/01 - 2010/12/31 PREVISÃO DE FUNÇÃO DE PROTEINAS POR MÉTODOS DE APRENDIZAGEM AUTOMÁTICA
SFRH/BD/29797/2006
Universidade de Lisboa Faculdade de Ciências, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Book
  1. Dragisic, Z.; Ivanova, V.; Lambrix, P.; Faria, D.; Jiménez-Ruiz, E.; Pesquita, C.. User validation in ontology alignment. 2016.
    10.1007/978-3-319-46523-4_13
  2. Pesquita, C.; Faria, D.; Santos, E.; Neefs, J.-M.; Couto, F.M.. Towards visualizing the alignment of large biomedical ontologies. 2014.
    10.1007/978-3-319-08590-6_10
  3. Faria, D.; Jiménez-Ruiz, E.; Pesquita, C.; Santos, E.; Couto, F.M.. Towards annotating potential incoherences in bioportal mappings. 2014.
  4. Pesquita, C.; Faria, D.; Stroe, C.; Santos, E.; Cruz, I.F.; Couto, F.M.. What's in a 'nym'? Synonyms in biomedical ontology matching. 2013.
    10.1007/978-3-642-41335-3_33
Book chapter
  1. Marta Contreiras Silva; Daniel Faria; Catia Pesquita. "Complex Multi-Ontology Alignment Through Geometric Operations on Language Embeddings". 2024.
    10.3233/FAIA240632
  2. Pommier, Cyril; Coppens, Frederik; Cwiek-Kupczynska, Hanna; Faria, Daniel; Beier, Sebastian; Miguel, Célia; Michotey, Célia; et al. Corresponding author: Pommier, Cyril. "Plant Science Data Integration, from Building Community Standards to Defining a Consistent Data Lifecycle". In Towards Responsible Plant Data Linkage: Data Challenges for Agricultural Research and Development, 149-160. Springer International Publishing, 2023.
    Published • 10.1007/978-3-031-13276-6_8
Conference paper
  1. Faria, Daniel; Balbi, Laura; Pesquita, Cátia; Giesteira Cotovio, Pedro; Ferraz, Lucas; Marta Silva. Corresponding author: Faria, Daniel. "Results for Matcha and Matcha-DL in OAEI 2023". Paper presented in The 18th International Workshop on Ontology Matching collocated with the 22nd International Semantic Web Conference ISWC-2023, Athens, 2023.
    Published
  2. Silva, Marta Contreiras; Faria, Daniel; Pesquita, Cátia. "Matching Multiple Ontologies to Build a Knowledge Graph for Personalized Medicine". Paper presented in European Semantic Web Conference (ESWC), Hersonissos, 2022.
    Accepted
  3. Faria, D.; Pesquita, C.; Tervo, T.; Couto, F.M.; Cruz, I.F.. "AML and AMLC results for OAEI 2019". 2019.
  4. Algergawy, A.; Faria, D.; Ferrara, A.; Fundulaki, I.; Harrow, I.; Hertling, S.; Jiménez-Ruiz, E.; et al. "Results of the ontology alignment evaluation initiative 2019". 2019.
  5. Jiménez-Ruiz, E.; Saveta, T.; Zamazal, O.; Hertling, S.; Röder, M.; Fundulaki, I.; Ngomo, A.-C.N.; et al. "Introducing the HOBBIT platform into the Ontology Alignment Evaluation campaign". 2018.
  6. Algergawy, A.; Cheatham, M.; Faria, D.; Ferrara, A.; Fundulaki, I.; Harrow, I.; Hertling, S.; et al. "Results of the ontology alignment evaluation initiative 2018". 2018.
  7. Faria, D.; Pesquita, C.; Balasubramani, B.S.; Tervo, T.; Carriço, D.; Garrilha, R.; Couto, F.M.; Cruz, I.F.. "Results of AML participation in OAEI2018". 2018.
  8. Cardoso, J.; Bakhshandeh, M.; Faria, D.; Pesquita, C.; Borbinha, J.. "Ontology-based approach for heterogeneity analysis of EA models". Paper presented in International Conference on Business Process Management, 2017.
    10.1007/978-3-319-58457-7_10
  9. Achichi, M.; Cheatham, M.; Dragisic, Z.; Euzenat, J.; Faria, D.; Ferrara, A.; Flouris, G.; et al. "Results of the ontology alignment evaluation initiative 2017?". 2017.
  10. Faria, D.; Balasubramani, B.S.; Shivaprabhu, V.R.; Mott, I.; Pesquita, C.; Couto, F.M.; Cruz, I.F.. "Results of AML in OAEI 2017". 2017.
  11. Achichi, M.; Cheatham, M.; Dragisic, Z.; Euzenat, J.; Faria, D.; Ferrara, A.; Flouris, G.; et al. "Results of the Ontology Alignment Evaluation Initiative 2016". 2016.
  12. Faria, D.; Pesquita, C.; Balasubramani, B.S.; Martins, C.; Cardoso, J.; Curado, H.; Couto, F.M.; Cruz, I.F.. "OAEI 2016 results of AML". 2016.
  13. Martins, C.; Faria, D.; Pesquita, C.. "Visualization and editing of biomedical ontology alignments in AgreementMakerLight". 2015.
  14. Cheatham, M.; Dragisic, Z.; Euzenat, J.; Faria, D.; Ferrara, A.; Flouris, G.; Fundulaki, I.; et al. "Results of the ontology alignment evaluation initiative 2015". 2015.
  15. Faria, D.; Martins, C.; Nanavaty, A.; Oliveira, D.; Balasubramani, B.S.; Taheri, A.; Pesquita, C.; Couto, F.M.; Cruz, I.F.. "AML results for OAEI 2015". 2015.
  16. Faria, D.; Martins, C.; Nanavaty, A.; Taheri, A.; Pesquita, C.; Santos, E.; Cruz, I.F.; Couto, F.M.. "Agreementmakerlight results for OAEI 2014". 2014.
  17. Pesquita, C.; Cheatham, M.; Faria, D.; Barros, J.; Santos, E.; Couto, F.M.. "Building reference alignments for compound matching of multiple ontologies using OBO cross-products". 2014.
  18. Faria, D.; Pesquita, C.; Santos, E.; Cruz, I.F.; Couto, F.M.. "AgreementMakerLight 2.0: Towards efficient large-scale ontology matching". 2014.
  19. Dragisic, Z.; Eckert, K.; Euzenat, J.; Faria, D.; Ferrara, A.; Granada, R.; Ivanova, V.; et al. "Results of the ontology alignment evaluation initiative 2014". 2014.
  20. Faria, D.; Pesquita, C.; Santos, E.; Cruz, I.F.; Couto, F.M.. "AgreementMakerLight results for OAEI 2013". 2013.
  21. Pesquita, C.; Faria, D.; Santos, E.; Couto, F.M.. "To repair or not to repair: Reconciling correctness and coherence in ontology reference alignments". 2013.
  22. Tavares, B.; Bastos, H.P.; Faria, D.; Ferreira, J.D.; Grego, T.; Pesquita, C.; Couto, F.M.. "The biomedical ontology applications (BOA) framework". 2011.
  23. Peneda, Jorge; Charro, Nuno; L. Hood, Brian; Fonseca, Aidil; Hagenfeldt, Manuela; Miranda, Armandina; Zerimech, Farid; et al. "Utilidade da Proteómica na Compreensão da Patogenia Molecular Proximal da Doença Cerebral Alcoólica". 2011.
Conference poster
  1. Barros, Pedro M.; Chaves, Inês; Costa, Bruno Vasques; Faria, Daniel; Marum, Liliana; Miguel, Célia M.; Saibo, Nelson; et al. "Data management in plant sciences: update on the BioData.pt Plant Sciences community". Paper presented in 1st All Hands / 3rd Technical Meeting of BIODATA.PT | ELIXIR PT, 2022.
    10.5281/zenodo.10467148
  2. Silva, Marta Contreiras; Faria, Daniel; Pesquita, Cátia. "Extending AgreementMakerLight to Perform Holistic Ontology Matching". Paper presented in 19th Extended Semantic Web Conference, 2022.
  3. Silva, Marta Contreiras; Faria, Daniel; Pesquita, Cátia. "Integrating knowledge graphs for explainable artificial intelligence in biomedicine". Paper presented in 16th International Workshop on Ontology Matching, 2021.
Journal article
  1. Faria, Daniel; Santos, Emanuel; Balasubramani, Booma Sowkarthiga; Silva, Marta C.; Couto, Francisco M.; Pesquita, Cátia. Corresponding author: Pesquita, Cátia. "AgreementMakerLight". Semantic Web (2023): 1-13. http://dx.doi.org/10.3233/sw-233304.
    10.3233/sw-233304
  2. Marta Contreiras Silva; Patrícia Eugénio; Daniel Faria; Catia Pesquita. "Ontologies and Knowledge Graphs in Oncology Research". Cancers (2022): https://doi.org/10.3390/cancers14081906.
    10.3390/cancers14081906
  3. Silva, Marta Contreiras; Eugénio, Patrícia; Faria, Daniel; Pesquita, Cátia. "Ontologies in oncology: a review of semantic technology applications in cancer research". Cancers MDPI (2022):
    Accepted
  4. "Vitamin D-related polymorphisms and vitamin D levels as risk biomarkers of COVID-19 disease severity". Scientific Reports 11 1 (2021): http://dx.doi.org/10.1038/s41598-021-99952-z.
    10.1038/s41598-021-99952-z
  5. "CorkOakDB—The Cork Oak Genome Database Portal". Database 2020 (2020): http://dx.doi.org/10.1093/database/baaa114.
    10.1093/database/baaa114
  6. Evangelia A. Papoutsoglou; Daniel Faria; Daniel Arend; Elizabeth Arnaud; Ioannis N. Athanasiadis; Inês Chaves; Frederik Coppens; et al. "Enabling reusability of plant phenomic datasets with MIAPPE 1.1". New Phytologist 227 1 (2020): 260-273. https://doi.org/10.1111/nph.16544.
    10.1111/nph.16544
  7. Faria, Daniel. "User validation in ontology alignment: functional assessment and impact". The Knowledge Engineering Review (2019): http://dx.doi.org/10.1017/s0269888919000080.
    10.1017/s0269888919000080
  8. Daniel Faria; Catia Pesquita; Isabela Mott; Catarina Martins; Francisco M. Couto; Isabel F. Cruz. "Tackling the challenges of matching biomedical ontologies". Journal of Biomedical Semantics 9 1 (2018): https://doi.org/10.1186/s13326-017-0170-9.
    10.1186/s13326-017-0170-9
  9. Santos, E.; Faria, D.; Pesquita, C.; Couto, F.M.. "Ontology alignment repair through modularization and confidence-based heuristics". PLoS ONE 10 12 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84957588757&partnerID=MN8TOARS.
    10.1371/journal.pone.0144807
  10. Faria, D.; Pesquita, C.; Santos, E.; Cruz, I.F.; Couto, F.M.. "Automatic background knowledge selection for matching biomedical ontologies". PLoS ONE 9 11 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84915758310&partnerID=MN8TOARS.
    10.1371/journal.pone.0111226
  11. Faria, D.; Pesquita, C.; Santos, E.; Palmonari, M.; Cruz, I.F.; Couto, F.M.. "The AgreementMakerLight ontology matching system". Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 8185 LNCS (2013): 527-541. http://www.scopus.com/inward/record.url?eid=2-s2.0-84886730657&partnerID=MN8TOARS.
    10.1007/978-3-642-41030-7_38
  12. Faria, D.; Schlicker, A.; Pesquita, C.; Bastos, H.; FerreiraAntó, A.E.N.; Albrecht, M.; Falcão, A.O.. "Mining GO annotations for improving annotation consistency". PLoS ONE 7 7 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84864674779&partnerID=MN8TOARS.
    10.1371/journal.pone.0040519
  13. Charro, N.; Hood, B.L.; Faria, D.; Pacheco, P.; Azevedo, P.; Lopes, C.; de Almeida, A.B.; et al. "Serum proteomics signature of Cystic Fibrosis patients: A complementary 2-DE and LC-MS/MS approach". Journal of Proteomics 74 1 (2011): 110-126. http://www.scopus.com/inward/record.url?eid=2-s2.0-78649872123&partnerID=MN8TOARS.
    10.1016/j.jprot.2010.10.001
  14. Bastos, H.P.; Tavares, B.; Pesquita, C.; Faria, D.; Couto, F.M.. "Application of gene ontology to gene identification". Methods in Molecular Biology 760 (2011): 141-157. http://www.scopus.com/inward/record.url?eid=2-s2.0-79960906222&partnerID=MN8TOARS.
    10.1007/978-1-61779-176-5_9
  15. Simões, T.; Charro, N.; Blonder, J.; Faria, D.; Couto, F.M.; Chan, K.C.; Waybright, T.; et al. "Molecular profiling of the human nasal epithelium: A proteomics approach". Journal of Proteomics 75 1 (2011): 56-69. http://www.scopus.com/inward/record.url?eid=2-s2.0-84858721493&partnerID=MN8TOARS.
    10.1016/j.jprot.2011.05.012
  16. Pesquita, C.; Faria, D.; Couto, F.M.. "Measuring coherence between electronic and manual annotations in biological databases". Proceedings of the ACM Symposium on Applied Computing (2009): 806-807. http://www.scopus.com/inward/record.url?eid=2-s2.0-72949093556&partnerID=MN8TOARS.
    10.1145/1529282.1529452
  17. Taylor, I.W.; Linding, R.; Warde-Farley, D.; Liu, Y.; Pesquita, C.; Faria, D.; Bull, S.; et al. "Dynamic modularity in protein interaction networks predicts breast cancer outcome". Nature Biotechnology 27 2 (2009): 199-204. http://www.scopus.com/inward/record.url?eid=2-s2.0-59849125136&partnerID=MN8TOARS.
    10.1038/nbt.1522
  18. Pesquita, C.; Faria, D.; Falcão, A.O.; Lord, P.; Couto, F.M.. "Semantic similarity in biomedical ontologies". PLoS Computational Biology 5 7 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-68249087607&partnerID=MN8TOARS.
    10.1371/journal.pcbi.1000443
  19. Faria, D.; Ferreira, A.E.N.; Falcão, A.O.. "Enzyme classification with peptide programs: A comparative study". BMC Bioinformatics 10 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-68949098339&partnerID=MN8TOARS.
    10.1186/1471-2105-10-231
  20. Pesquita, C.; Faria, D.; Bastos, H.; Ferreira, A.E.N.; Falcão, A.O.; Couto, F.M.. "Metrics for GO based protein semantic similarity: A systematic evaluation". BMC Bioinformatics 9 SUPPL. 5 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-47149083877&partnerID=MN8TOARS.
    10.1186/1471-2105-9-S5-S4
  21. Bastos, H.P.; Pesquita, C.; Faria, D.; Falcão, A.O.. "BOLOS: BLAST & ontology linked-hOmologue stars". Proceedings of the ACM Symposium on Applied Computing (2008): 1278-1281. http://www.scopus.com/inward/record.url?eid=2-s2.0-56749095713&partnerID=MN8TOARS.
    10.1145/1363686.1363982
  22. Falcao, A.O.; Faria, D.; Ferreira, A.. "Peptide programs: Applying fragment programs to protein classification". International Conference on Information and Knowledge Management, Proceedings (2008): 37-44. http://www.scopus.com/inward/record.url?eid=2-s2.0-68949093215&partnerID=MN8TOARS.
    10.1145/1458449.1458459
Newspaper article
  1. Pesquita, Cátia; Faria, Daniel; Balbi, Laura; Eugénio, Patrícia; Bedran, George; Adrian Kallor, Ashwin; Nunes, Susana; et al. Corresponding author: Pesquita, Cátia. "The Immunopeptidomics Ontology (ImPO)", Database: The Journal of Biological Databases and Curation, 2024, https://doi.org/10.1093/database/baae014.
    https://doi.org/10.1093/database/baae014
  2. Giesteira Cotovio, Pedro; Ferraz, Lucas; Balbi, Laura; Pesquita, Cátia; Faria, Daniel. Corresponding author: Giesteira Cotovio, Pedro. "Matcha-DL a tool for supervised ontology alignment", Semantic Web, 2024, https://www.semantic-web-journal.net/content/matcha-dl-tool-supervised-ontology-alignment.
Online resource
  1. Costa, Bruno Vasques; Faria, Daniel; Chaves, Inês; Miguel, Célia Miguel. PHENO - the BrAPI endpoint provided by the Portuguese node of ELIXIR. https://brapi.biodata.pt. 2018. https://brapi.biodata.pt.
  2. Miguel, Célia; Bruno Vasques Costa; Faria, Daniel; Chaves, Inês; André Cordeiro. PHENO. 2018. https://brapi.biodata.pt.
Website
  1. Silva, Marta Contreiras; Faria, Daniel. BioData.pt Service Hub. 2020. http://services.biodata.pt/.
  2. Silva, Marta; Faria, Daniel; João Cardoso. Website for Ready for BioData Management - Workshop in Data Management. 2019. http://ready4biodatamanagement.biodata.pt/.

Other

Dataset
  1. Pesquita, Cátia; Faria, Daniel; Marta Contreiras Silva; Laura Balbi; Patrícia Eugénio. ImPO: Immunopeptidomics Ontology. 2023.
    10.5281/zenodo.8048222
Other output
  1. AgreementMakerLight - Ontology and Knowledge Graph Alignment Tool. Citations to associated publications: >700 AML is an open-source ontology matching system, currently one of the top ontology and knowledge graph matching systems consistently placing in the top tier of all tracks at the Ontology Alignment Evaluation Initiative (http://oaei.ontologymatching.org/). It has been used by NASA, Jansen Pharmaceuticals and FAO (United Nations) among others.. 2022. Pesquita, Cátia; Faria, Daniel. https://github.com/AgreementMakerLight.
  2. RDMkit. Web portal with guidelines and good data management practices for enabling FAIR data by design. 2021. https://rdmkit.elixir-europe.org/.
  3. CorkOakDB. Genome portal for Quercus suber. 2020. http://www.corkoakdb.org/.
  4. CorkOakDB website. CorkOakDB aims to integrate the knowledge generated from fundamental and applied studies about Quercus suber, with a focus on genetics. CorkOakDB features the first draft genome of Quercus suber, released in 2018 by the GENOSUBER consortium, and allows genome browsing and gene search. It also incorporates other types of data from cork oak scientific research, including gene expression data.. 2019. Barias-Aldrich, C; Silva, Marta C.; Barros, P.M.; Faria, Daniel; Sobral, Daniel. http://corkoakdb.org/.
Standard or policy
  1. MIAPPE: Minimal Information About Plant Phenotyping Experiments. 2019. https://www.miappe.org/.
Activities

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2021/02/01 - Current Distributed Knowledge Graphs for Biomedical Explainable Artificial Intelligence
Co-supervisor
Universidade de Lisboa Faculdade de Ciências, Portugal
2016/09/01 - 2022/07/31 Addressing Research Data Management with Semantic Technology
Co-supervisor
Universidade de Lisboa Instituto Superior Técnico, Portugal

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2019/07/17 Computational approaches to virtual screening in human central nervous system therapeutic targets
(Thesis) Arguer
 Samina Kausar (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal

Committee member

Activity description
Role 		Institution / Organization
2014/01/01 - Current Organizing committee of the annual Ontology Alignment Evaluation Initiative
Member

Conference scientific committee

Conference name Conference host
2016/01/01 - Current Extended Semantic Web Conference (ESWC)
2015/03/01 - Current Ontology Matching Workshop